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From: Jason Swails <jason.swails.gmail.com>

Date: Wed, 14 Jul 2010 15:30:32 -0400

Hello,

I believe this corresponds to the quasi-harmonic approximation to the entropy, right? I think if you do it correctly, ptraj will calculate the entropy for you. This is actually done in MMPBSA.py by setting entropy=1 in the input file. You don't have to use that script, but the code will show you how to do it.

Good luck!

Jason

Date: Wed, 14 Jul 2010 15:30:32 -0400

Hello,

I believe this corresponds to the quasi-harmonic approximation to the entropy, right? I think if you do it correctly, ptraj will calculate the entropy for you. This is actually done in MMPBSA.py by setting entropy=1 in the input file. You don't have to use that script, but the code will show you how to do it.

Good luck!

Jason

-- Jason Swails Quantum Theory Project, University of Florida Ph.D. Graduate Student 352-392-4032 On Jul 14, 2010, at 12:50 PM, Lekpa Duukori <duukori.gmail.com> wrote: > Hello, > > I am having some trouble with some analysis on mass weighted covariance > matrix from ptraj > > I am trying to get entropy estimates using the Schlitter formula (Chem Phys > Lett, 1993,215,617). I first do an rms fit to the first frame of my data > using the following ptraj commands ( I am using AmberTools 1.2) > > trajin model.mdcrd.nowaters > trajout model.mdcrd.fit > rms first mass out rms.out.fit > > Then do > > trajin model.mdcrd.fit > matrix mwcovar out mwcovar.out > > I then use the following python script to calculate the entropy > > #!/usr/bin/python > import numpy > sigma = numpy.loadtxt('mwcovar.out') > hbar = 1.054571628e-34 #Joules seconds > T = 300.0 # Kelvin > Kb = 1.3806504e-23 #Joules/Kelvin > Euler = numpy.exp(1) > constant = 10e-23 #Angstroms squared multiplied by g --> Kg (10^-3) > > unit_matrix = numpy.eye(len(sigma[0]),len(sigma[0]),dtype=float) > > matrix = unit_matrix + ((Kb*T*Euler*Euler)/(hbar*hbar))*sigma*constant > Entropy = 0.5*Kb*numpy.log(numpy.linalg.det(matrix)) > > But I get an infinite determinant and a NaN entropy, the elements matrix are > very large (10^26 or so, see below) > > I have done some dimensional analysis and think my units should be ok, but > the values in the matrix indicates otherwise so I don't know exactly what is > going wrong here. Any comments welcome. > > Thanks. > > Lekpa > > mwcovar matrix > [[ 0.75 -0.541 0.269 ..., 0.232 -0.571 0.065] > [-0.541 0.894 -0.4 ..., -0.597 0.793 -0.113] > [ 0.269 -0.4 1.099 ..., 0.354 -0.537 0.167] > ..., > [ 0.232 -0.597 0.354 ..., 1.102 -0.755 -0.031] > [-0.571 0.793 -0.537 ..., -0.755 1.762 -0.103] > [ 0.065 -0.113 0.167 ..., -0.031 -0.103 0.491]] > > > Output of python script > > [[ 2.06396838e+26 -1.48880919e+26 7.40276658e+25 ..., 6.38454218e+25 > -1.57136792e+26 1.78877259e+25] > [ -1.48880919e+26 2.46025031e+26 -1.10078313e+26 ..., -1.64291883e+26 > 2.18230256e+26 -3.10971236e+25] > [ 7.40276658e+25 -1.10078313e+26 3.02440166e+26 ..., 9.74193074e+25 > -1.47780136e+26 4.59576959e+25] > ..., > [ 6.38454218e+25 -1.64291883e+26 9.74193074e+25 ..., 3.03265754e+26 > -2.07772817e+26 -8.53106929e+24] > [ -1.57136792e+26 2.18230256e+26 -1.47780136e+26 ..., -2.07772817e+26 > 4.84894971e+26 -2.83451657e+25] > [ 1.78877259e+25 -3.10971236e+25 4.59576959e+25 ..., -8.53106929e+24 > -2.83451657e+25 1.35121130e+26]] > -inf > Entropy = nan > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Jul 14 2010 - 13:00:03 PDT

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